Starting phenix.real_space_refine on Sun Sep 29 09:10:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/09_2024/8gka_40181.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14361 2.51 5 N 3409 2.21 5 O 3884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 354 Unusual residues: {' NA': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 435 Unusual residues: {'POV': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 291 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 15.08, per 1000 atoms: 0.69 Number of scatterers: 21812 At special positions: 0 Unit cell: (164.628, 164.628, 129.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 33 15.00 Na 1 11.00 O 3884 8.00 N 3409 7.00 C 14361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.9 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 64.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.586A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.955A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.897A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 483 through 509 removed outlier: 3.540A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 3.546A pdb=" N ASP A 379 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 721 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 731 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP B 379 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 721 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS B 731 " --> pdb=" O GLU B 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP C 379 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS C 721 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS C 731 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 3.548A pdb=" N ASP D 379 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS D 721 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS D 731 " --> pdb=" O GLU D 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.45: 5647 1.45 - 1.57: 12727 1.57 - 1.69: 66 1.69 - 1.81: 204 Bond restraints: 22222 Sorted by residual: bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.77e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.38e-01 bond pdb=" CB PRO C 510 " pdb=" CG PRO C 510 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.36e-01 ... (remaining 22217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 29597 1.60 - 3.20: 176 3.20 - 4.79: 33 4.79 - 6.39: 8 6.39 - 7.99: 8 Bond angle restraints: 29822 Sorted by residual: angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA LEU D 608 " pdb=" CB LEU D 608 " pdb=" CG LEU D 608 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 ... (remaining 29817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12994 24.39 - 48.78: 433 48.78 - 73.18: 131 73.18 - 97.57: 17 97.57 - 121.96: 6 Dihedral angle restraints: 13581 sinusoidal: 6221 harmonic: 7360 Sorted by residual: dihedral pdb=" C27 POV B 803 " pdb=" C28 POV B 803 " pdb=" C29 POV B 803 " pdb="C210 POV B 803 " ideal model delta sinusoidal sigma weight residual 127.48 -110.56 -121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C27 POV A 809 " pdb=" C28 POV A 809 " pdb=" C29 POV A 809 " pdb="C210 POV A 809 " ideal model delta sinusoidal sigma weight residual 127.48 -116.73 -115.79 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C3 POV B 808 " pdb=" C31 POV B 808 " pdb=" O31 POV B 808 " pdb=" C32 POV B 808 " ideal model delta sinusoidal sigma weight residual 172.61 -76.70 -110.69 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2038 0.024 - 0.047: 729 0.047 - 0.071: 342 0.071 - 0.095: 83 0.095 - 0.119: 41 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA ILE B 734 " pdb=" N ILE B 734 " pdb=" C ILE B 734 " pdb=" CB ILE B 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3230 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5905 2.81 - 3.33: 21514 3.33 - 3.86: 35968 3.86 - 4.38: 44100 4.38 - 4.90: 74799 Nonbonded interactions: 182286 Sorted by model distance: nonbonded pdb=" O GLY B 638 " pdb="NA NA A 801 " model vdw 2.291 2.470 nonbonded pdb=" O GLY C 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY A 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY D 638 " pdb="NA NA A 801 " model vdw 2.293 2.470 nonbonded pdb=" NZ LYS C 589 " pdb=" O14 POV C 805 " model vdw 2.297 3.120 ... (remaining 182281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or resid 805 or (resid 806 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'B' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.180 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 22222 Z= 0.092 Angle : 0.385 7.989 29822 Z= 0.190 Chirality : 0.032 0.119 3233 Planarity : 0.002 0.030 3600 Dihedral : 13.139 121.958 8793 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2484 helix: 1.20 (0.13), residues: 1556 sheet: 3.44 (0.63), residues: 64 loop : -1.31 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 739 HIS 0.002 0.000 HIS C 301 PHE 0.004 0.001 PHE D 377 TYR 0.006 0.001 TYR D 208 ARG 0.002 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 460 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.7128 (mppt) cc_final: 0.6923 (mppt) REVERT: A 346 GLN cc_start: 0.8610 (mt0) cc_final: 0.7975 (mt0) REVERT: A 351 MET cc_start: 0.9254 (mtp) cc_final: 0.9013 (mtp) REVERT: A 514 GLN cc_start: 0.5620 (mm-40) cc_final: 0.5380 (tt0) REVERT: A 562 MET cc_start: 0.8987 (mmt) cc_final: 0.8652 (mmt) REVERT: B 253 LYS cc_start: 0.7125 (mppt) cc_final: 0.6922 (mppt) REVERT: B 346 GLN cc_start: 0.8626 (mt0) cc_final: 0.7990 (mt0) REVERT: B 351 MET cc_start: 0.9247 (mtp) cc_final: 0.9003 (mtp) REVERT: B 562 MET cc_start: 0.9015 (mmt) cc_final: 0.8728 (mmt) REVERT: B 680 THR cc_start: 0.8279 (p) cc_final: 0.8048 (m) REVERT: C 346 GLN cc_start: 0.8631 (mt0) cc_final: 0.7984 (mt0) REVERT: C 351 MET cc_start: 0.9252 (mtp) cc_final: 0.9010 (mtp) REVERT: C 562 MET cc_start: 0.9012 (mmt) cc_final: 0.8730 (mmt) REVERT: C 680 THR cc_start: 0.8274 (p) cc_final: 0.8054 (m) REVERT: D 346 GLN cc_start: 0.8630 (mt0) cc_final: 0.7996 (mt0) REVERT: D 351 MET cc_start: 0.9253 (mtp) cc_final: 0.9014 (mtp) REVERT: D 562 MET cc_start: 0.8992 (mmt) cc_final: 0.8687 (mmt) REVERT: D 680 THR cc_start: 0.8287 (p) cc_final: 0.8071 (m) outliers start: 12 outliers final: 4 residues processed: 468 average time/residue: 1.4253 time to fit residues: 750.1714 Evaluate side-chains 313 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 205 ASN A 279 GLN A 580 GLN A 645 GLN B 182 ASN B 279 GLN B 570 GLN B 580 GLN B 645 GLN B 647 ASN B 695 GLN C 182 ASN C 279 GLN C 580 GLN C 645 GLN C 695 GLN D 182 ASN D 279 GLN D 580 GLN D 645 GLN D 695 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22222 Z= 0.294 Angle : 0.642 11.563 29822 Z= 0.320 Chirality : 0.041 0.147 3233 Planarity : 0.004 0.037 3600 Dihedral : 16.704 132.643 3893 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.20 % Allowed : 10.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2484 helix: 1.28 (0.12), residues: 1604 sheet: 3.12 (0.65), residues: 64 loop : -1.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 692 HIS 0.007 0.001 HIS B 301 PHE 0.016 0.002 PHE A 526 TYR 0.019 0.003 TYR A 321 ARG 0.003 0.001 ARG C 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 331 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6876 (mmm) cc_final: 0.6331 (mmm) REVERT: A 185 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 351 MET cc_start: 0.9282 (mtp) cc_final: 0.9072 (mtp) REVERT: A 378 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8833 (t) REVERT: A 562 MET cc_start: 0.9160 (mmt) cc_final: 0.8740 (mmt) REVERT: A 740 THR cc_start: 0.7882 (m) cc_final: 0.7630 (p) REVERT: B 159 MET cc_start: 0.6707 (mmm) cc_final: 0.5986 (mmm) REVERT: B 185 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 351 MET cc_start: 0.9276 (mtp) cc_final: 0.9063 (mtp) REVERT: B 378 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8838 (t) REVERT: B 514 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6648 (mm-40) REVERT: B 562 MET cc_start: 0.9170 (mmt) cc_final: 0.8695 (mmt) REVERT: B 740 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7643 (p) REVERT: C 159 MET cc_start: 0.6899 (mmm) cc_final: 0.6015 (mmm) REVERT: C 185 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7028 (mm-30) REVERT: C 351 MET cc_start: 0.9277 (mtp) cc_final: 0.9062 (mtp) REVERT: C 378 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (t) REVERT: C 514 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6593 (mm-40) REVERT: C 562 MET cc_start: 0.9173 (mmt) cc_final: 0.8678 (mmt) REVERT: C 740 THR cc_start: 0.7954 (m) cc_final: 0.7693 (p) REVERT: D 159 MET cc_start: 0.6711 (mmm) cc_final: 0.5999 (mmm) REVERT: D 185 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7035 (mm-30) REVERT: D 346 GLN cc_start: 0.9119 (mt0) cc_final: 0.8399 (mt0) REVERT: D 351 MET cc_start: 0.9282 (mtp) cc_final: 0.9071 (mtp) REVERT: D 378 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8837 (t) REVERT: D 514 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6707 (mm-40) REVERT: D 562 MET cc_start: 0.9160 (mmt) cc_final: 0.8652 (mmt) REVERT: D 740 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (p) outliers start: 71 outliers final: 22 residues processed: 388 average time/residue: 1.5117 time to fit residues: 657.1466 Evaluate side-chains 316 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 285 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 243 optimal weight: 0.0970 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 180 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 695 GLN B 452 ASN B 570 GLN C 452 ASN D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22222 Z= 0.144 Angle : 0.507 10.583 29822 Z= 0.254 Chirality : 0.036 0.140 3233 Planarity : 0.003 0.024 3600 Dihedral : 16.158 121.813 3893 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.20 % Allowed : 12.09 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2484 helix: 1.56 (0.13), residues: 1604 sheet: 3.56 (0.65), residues: 64 loop : -1.44 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 380 HIS 0.005 0.001 HIS D 301 PHE 0.015 0.001 PHE C 193 TYR 0.014 0.001 TYR B 208 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 315 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6859 (mmm) cc_final: 0.6566 (mmm) REVERT: A 185 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 378 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 562 MET cc_start: 0.9158 (mmt) cc_final: 0.8717 (mmt) REVERT: A 686 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8291 (ptpp) REVERT: A 740 THR cc_start: 0.7909 (m) cc_final: 0.7502 (p) REVERT: B 159 MET cc_start: 0.6771 (mmm) cc_final: 0.6382 (mmm) REVERT: B 185 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6942 (mm-30) REVERT: B 378 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8896 (t) REVERT: B 447 PHE cc_start: 0.8652 (m-80) cc_final: 0.8434 (m-10) REVERT: B 562 MET cc_start: 0.9146 (mmt) cc_final: 0.8837 (mmt) REVERT: B 686 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: B 740 THR cc_start: 0.7903 (m) cc_final: 0.7497 (p) REVERT: C 159 MET cc_start: 0.6940 (mmm) cc_final: 0.6480 (mmm) REVERT: C 185 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6893 (mm-30) REVERT: C 283 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: C 378 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8899 (t) REVERT: C 562 MET cc_start: 0.9154 (mmt) cc_final: 0.8758 (mmt) REVERT: C 619 CYS cc_start: 0.6390 (p) cc_final: 0.6097 (p) REVERT: C 686 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8310 (ptpp) REVERT: C 740 THR cc_start: 0.7904 (m) cc_final: 0.7501 (p) REVERT: D 159 MET cc_start: 0.6774 (mmm) cc_final: 0.6385 (mmm) REVERT: D 185 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7024 (mm-30) REVERT: D 346 GLN cc_start: 0.9085 (mt0) cc_final: 0.8412 (mt0) REVERT: D 378 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8898 (t) REVERT: D 562 MET cc_start: 0.9141 (mmt) cc_final: 0.8720 (mmt) REVERT: D 619 CYS cc_start: 0.6491 (p) cc_final: 0.6194 (p) REVERT: D 686 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8342 (ptpp) REVERT: D 740 THR cc_start: 0.7895 (m) cc_final: 0.7490 (p) outliers start: 71 outliers final: 21 residues processed: 369 average time/residue: 1.4938 time to fit residues: 618.4476 Evaluate side-chains 319 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 289 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 214 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 647 ASN B 279 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22222 Z= 0.177 Angle : 0.541 10.842 29822 Z= 0.268 Chirality : 0.037 0.143 3233 Planarity : 0.003 0.026 3600 Dihedral : 16.019 117.153 3885 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.84 % Allowed : 13.54 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2484 helix: 1.57 (0.12), residues: 1624 sheet: 3.57 (0.64), residues: 64 loop : -1.42 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 380 HIS 0.006 0.001 HIS A 301 PHE 0.013 0.001 PHE A 193 TYR 0.013 0.002 TYR C 208 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 303 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6901 (mm-30) REVERT: A 378 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8874 (t) REVERT: A 488 MET cc_start: 0.6559 (mmt) cc_final: 0.6262 (mtm) REVERT: A 562 MET cc_start: 0.9155 (mmt) cc_final: 0.8690 (mmt) REVERT: A 686 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8379 (ptpp) REVERT: A 740 THR cc_start: 0.7978 (m) cc_final: 0.7552 (p) REVERT: B 159 MET cc_start: 0.6785 (mmm) cc_final: 0.6501 (mmm) REVERT: B 185 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 378 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8875 (t) REVERT: B 447 PHE cc_start: 0.8668 (m-80) cc_final: 0.8455 (m-10) REVERT: B 488 MET cc_start: 0.6474 (mmt) cc_final: 0.6176 (mtm) REVERT: B 562 MET cc_start: 0.9178 (mmt) cc_final: 0.8796 (mmt) REVERT: B 686 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8379 (ptpp) REVERT: B 740 THR cc_start: 0.7979 (m) cc_final: 0.7546 (p) REVERT: C 159 MET cc_start: 0.6990 (mmm) cc_final: 0.6306 (mmm) REVERT: C 185 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 283 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: C 378 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8885 (t) REVERT: C 562 MET cc_start: 0.9164 (mmt) cc_final: 0.8733 (mmt) REVERT: C 619 CYS cc_start: 0.6470 (p) cc_final: 0.6181 (p) REVERT: C 686 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8384 (ptpp) REVERT: C 740 THR cc_start: 0.7988 (m) cc_final: 0.7577 (p) REVERT: D 159 MET cc_start: 0.6737 (mmm) cc_final: 0.6470 (mmm) REVERT: D 283 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: D 346 GLN cc_start: 0.9084 (mt0) cc_final: 0.8355 (mt0) REVERT: D 378 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8891 (t) REVERT: D 488 MET cc_start: 0.6505 (mmt) cc_final: 0.6205 (mtm) REVERT: D 562 MET cc_start: 0.9154 (mmt) cc_final: 0.8694 (mmt) REVERT: D 619 CYS cc_start: 0.6500 (p) cc_final: 0.6209 (p) REVERT: D 686 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8425 (ptpp) REVERT: D 740 THR cc_start: 0.7980 (m) cc_final: 0.7550 (p) outliers start: 63 outliers final: 27 residues processed: 344 average time/residue: 1.5571 time to fit residues: 597.7453 Evaluate side-chains 322 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 3 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN C 279 GLN C 750 ASN D 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22222 Z= 0.161 Angle : 0.524 10.713 29822 Z= 0.261 Chirality : 0.037 0.142 3233 Planarity : 0.003 0.026 3600 Dihedral : 15.841 118.311 3885 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.48 % Allowed : 14.71 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2484 helix: 1.66 (0.12), residues: 1616 sheet: 3.50 (0.64), residues: 64 loop : -1.43 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 710 HIS 0.006 0.001 HIS B 301 PHE 0.011 0.001 PHE D 193 TYR 0.013 0.001 TYR A 208 ARG 0.002 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 306 time to evaluate : 2.618 Fit side-chains REVERT: A 283 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: A 378 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 447 PHE cc_start: 0.8637 (m-80) cc_final: 0.8432 (m-10) REVERT: A 488 MET cc_start: 0.6547 (mmt) cc_final: 0.6278 (mtm) REVERT: A 562 MET cc_start: 0.9159 (mmt) cc_final: 0.8702 (mmt) REVERT: A 618 ASP cc_start: 0.7136 (m-30) cc_final: 0.6831 (m-30) REVERT: A 619 CYS cc_start: 0.6457 (p) cc_final: 0.6145 (p) REVERT: A 686 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8476 (ptpp) REVERT: A 740 THR cc_start: 0.7898 (m) cc_final: 0.7519 (p) REVERT: B 159 MET cc_start: 0.6841 (mmm) cc_final: 0.6578 (mmm) REVERT: B 283 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: B 378 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8847 (t) REVERT: B 447 PHE cc_start: 0.8662 (m-80) cc_final: 0.8442 (m-10) REVERT: B 488 MET cc_start: 0.6468 (mmt) cc_final: 0.6176 (mtm) REVERT: B 562 MET cc_start: 0.9168 (mmt) cc_final: 0.8817 (mmt) REVERT: B 619 CYS cc_start: 0.6437 (p) cc_final: 0.6123 (p) REVERT: B 740 THR cc_start: 0.7897 (m) cc_final: 0.7508 (p) REVERT: C 159 MET cc_start: 0.7000 (mmm) cc_final: 0.6401 (mmm) REVERT: C 283 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: C 378 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8879 (t) REVERT: C 447 PHE cc_start: 0.8607 (m-80) cc_final: 0.8401 (m-10) REVERT: C 488 MET cc_start: 0.6568 (mmt) cc_final: 0.6265 (mtm) REVERT: C 562 MET cc_start: 0.9172 (mmt) cc_final: 0.8758 (mmt) REVERT: C 618 ASP cc_start: 0.7086 (m-30) cc_final: 0.6777 (m-30) REVERT: C 619 CYS cc_start: 0.6492 (p) cc_final: 0.6198 (p) REVERT: C 740 THR cc_start: 0.7902 (m) cc_final: 0.7525 (p) REVERT: D 159 MET cc_start: 0.6814 (mmm) cc_final: 0.6303 (mmm) REVERT: D 283 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: D 346 GLN cc_start: 0.9078 (mt0) cc_final: 0.8309 (mt0) REVERT: D 378 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8855 (t) REVERT: D 488 MET cc_start: 0.6561 (mmt) cc_final: 0.6281 (mtm) REVERT: D 514 GLN cc_start: 0.7015 (tt0) cc_final: 0.6622 (mm-40) REVERT: D 562 MET cc_start: 0.9155 (mmt) cc_final: 0.8717 (mmt) REVERT: D 618 ASP cc_start: 0.7080 (m-30) cc_final: 0.6777 (m-30) REVERT: D 619 CYS cc_start: 0.6518 (p) cc_final: 0.6224 (p) REVERT: D 740 THR cc_start: 0.7882 (m) cc_final: 0.7492 (p) outliers start: 55 outliers final: 28 residues processed: 346 average time/residue: 1.6071 time to fit residues: 619.8011 Evaluate side-chains 324 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 287 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN C 279 GLN C 750 ASN D 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22222 Z= 0.182 Angle : 0.551 11.452 29822 Z= 0.273 Chirality : 0.037 0.145 3233 Planarity : 0.003 0.026 3600 Dihedral : 15.838 117.079 3885 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2484 helix: 1.65 (0.12), residues: 1624 sheet: 3.30 (0.64), residues: 64 loop : -1.43 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.010 0.001 PHE A 193 TYR 0.013 0.002 TYR A 208 ARG 0.002 0.000 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 304 time to evaluate : 2.260 Fit side-chains REVERT: A 283 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: A 447 PHE cc_start: 0.8641 (m-80) cc_final: 0.8430 (m-10) REVERT: A 488 MET cc_start: 0.6549 (mmt) cc_final: 0.6283 (mtm) REVERT: A 562 MET cc_start: 0.9166 (mmt) cc_final: 0.8701 (mmt) REVERT: A 618 ASP cc_start: 0.7168 (m-30) cc_final: 0.6868 (m-30) REVERT: A 619 CYS cc_start: 0.6463 (p) cc_final: 0.6153 (p) REVERT: A 740 THR cc_start: 0.7939 (m) cc_final: 0.7541 (p) REVERT: B 159 MET cc_start: 0.6952 (mmm) cc_final: 0.6437 (mmm) REVERT: B 283 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 447 PHE cc_start: 0.8665 (m-80) cc_final: 0.8445 (m-10) REVERT: B 488 MET cc_start: 0.6552 (mmt) cc_final: 0.6275 (mtm) REVERT: B 562 MET cc_start: 0.9184 (mmt) cc_final: 0.8798 (mmt) REVERT: B 618 ASP cc_start: 0.7163 (m-30) cc_final: 0.6856 (m-30) REVERT: B 619 CYS cc_start: 0.6442 (p) cc_final: 0.6133 (p) REVERT: B 740 THR cc_start: 0.7858 (m) cc_final: 0.7443 (p) REVERT: C 159 MET cc_start: 0.7081 (mmm) cc_final: 0.6490 (mmm) REVERT: C 283 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: C 447 PHE cc_start: 0.8622 (m-80) cc_final: 0.8412 (m-10) REVERT: C 488 MET cc_start: 0.6577 (mmt) cc_final: 0.6288 (mtm) REVERT: C 562 MET cc_start: 0.9181 (mmt) cc_final: 0.8758 (mmt) REVERT: C 618 ASP cc_start: 0.7150 (m-30) cc_final: 0.6844 (m-30) REVERT: C 619 CYS cc_start: 0.6504 (p) cc_final: 0.6213 (p) REVERT: C 740 THR cc_start: 0.7951 (m) cc_final: 0.7565 (p) REVERT: D 159 MET cc_start: 0.6933 (mmm) cc_final: 0.6452 (mmm) REVERT: D 283 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: D 346 GLN cc_start: 0.9081 (mt0) cc_final: 0.8299 (mt0) REVERT: D 488 MET cc_start: 0.6578 (mmt) cc_final: 0.6311 (mtm) REVERT: D 514 GLN cc_start: 0.7024 (tt0) cc_final: 0.6626 (mm-40) REVERT: D 562 MET cc_start: 0.9155 (mmt) cc_final: 0.8715 (mmt) REVERT: D 618 ASP cc_start: 0.7115 (m-30) cc_final: 0.6818 (m-30) REVERT: D 619 CYS cc_start: 0.6508 (p) cc_final: 0.6211 (p) REVERT: D 740 THR cc_start: 0.7952 (m) cc_final: 0.7543 (p) outliers start: 46 outliers final: 20 residues processed: 339 average time/residue: 1.6185 time to fit residues: 611.1043 Evaluate side-chains 318 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22222 Z= 0.178 Angle : 0.557 11.222 29822 Z= 0.275 Chirality : 0.038 0.154 3233 Planarity : 0.003 0.026 3600 Dihedral : 15.766 117.532 3885 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.21 % Allowed : 15.43 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2484 helix: 1.65 (0.12), residues: 1620 sheet: 3.24 (0.64), residues: 64 loop : -1.39 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 710 HIS 0.006 0.001 HIS C 301 PHE 0.012 0.001 PHE C 377 TYR 0.013 0.002 TYR A 208 ARG 0.002 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 312 time to evaluate : 2.350 Fit side-chains REVERT: A 156 ASP cc_start: 0.5349 (t0) cc_final: 0.5140 (OUTLIER) REVERT: A 283 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: A 447 PHE cc_start: 0.8636 (m-80) cc_final: 0.8429 (m-10) REVERT: A 488 MET cc_start: 0.6567 (mmt) cc_final: 0.6295 (mtm) REVERT: A 562 MET cc_start: 0.9173 (mmt) cc_final: 0.8716 (mmt) REVERT: A 618 ASP cc_start: 0.7177 (m-30) cc_final: 0.6875 (m-30) REVERT: A 619 CYS cc_start: 0.6460 (p) cc_final: 0.6152 (p) REVERT: A 740 THR cc_start: 0.7923 (m) cc_final: 0.7549 (p) REVERT: B 159 MET cc_start: 0.6961 (mmm) cc_final: 0.6446 (mmm) REVERT: B 263 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: B 283 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: B 447 PHE cc_start: 0.8661 (m-80) cc_final: 0.8443 (m-10) REVERT: B 488 MET cc_start: 0.6561 (mmt) cc_final: 0.6289 (mtm) REVERT: B 562 MET cc_start: 0.9183 (mmt) cc_final: 0.8814 (mmt) REVERT: B 618 ASP cc_start: 0.7177 (m-30) cc_final: 0.6869 (m-30) REVERT: B 619 CYS cc_start: 0.6506 (p) cc_final: 0.6189 (p) REVERT: B 686 LYS cc_start: 0.8840 (ptpp) cc_final: 0.8143 (mttp) REVERT: B 740 THR cc_start: 0.7843 (m) cc_final: 0.7476 (p) REVERT: C 159 MET cc_start: 0.7147 (mmm) cc_final: 0.6289 (mmm) REVERT: C 283 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: C 447 PHE cc_start: 0.8615 (m-80) cc_final: 0.8406 (m-10) REVERT: C 488 MET cc_start: 0.6589 (mmt) cc_final: 0.6308 (mtm) REVERT: C 562 MET cc_start: 0.9182 (mmt) cc_final: 0.8763 (mmt) REVERT: C 618 ASP cc_start: 0.7156 (m-30) cc_final: 0.6851 (m-30) REVERT: C 619 CYS cc_start: 0.6544 (p) cc_final: 0.6235 (p) REVERT: C 686 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8138 (mttp) REVERT: C 740 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7567 (p) REVERT: D 159 MET cc_start: 0.6934 (mmm) cc_final: 0.6401 (mmm) REVERT: D 283 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: D 346 GLN cc_start: 0.9078 (mt0) cc_final: 0.8297 (mt0) REVERT: D 488 MET cc_start: 0.6590 (mmt) cc_final: 0.6319 (mtm) REVERT: D 562 MET cc_start: 0.9156 (mmt) cc_final: 0.8718 (mmt) REVERT: D 618 ASP cc_start: 0.7127 (m-30) cc_final: 0.6828 (m-30) REVERT: D 619 CYS cc_start: 0.6479 (p) cc_final: 0.6176 (p) REVERT: D 686 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8165 (mttp) REVERT: D 740 THR cc_start: 0.7910 (m) cc_final: 0.7523 (p) outliers start: 49 outliers final: 21 residues processed: 348 average time/residue: 1.5993 time to fit residues: 621.7208 Evaluate side-chains 331 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 205 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22222 Z= 0.175 Angle : 0.558 11.287 29822 Z= 0.276 Chirality : 0.037 0.150 3233 Planarity : 0.003 0.029 3600 Dihedral : 15.715 117.479 3885 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.12 % Allowed : 16.06 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2484 helix: 1.68 (0.12), residues: 1620 sheet: 3.26 (0.64), residues: 64 loop : -1.39 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 710 HIS 0.006 0.001 HIS D 301 PHE 0.014 0.001 PHE C 377 TYR 0.013 0.002 TYR B 208 ARG 0.001 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 318 time to evaluate : 2.180 Fit side-chains REVERT: A 283 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 447 PHE cc_start: 0.8637 (m-80) cc_final: 0.8428 (m-10) REVERT: A 488 MET cc_start: 0.6564 (mmt) cc_final: 0.6296 (mtm) REVERT: A 562 MET cc_start: 0.9171 (mmt) cc_final: 0.8725 (mmt) REVERT: A 618 ASP cc_start: 0.7195 (m-30) cc_final: 0.6902 (m-30) REVERT: A 619 CYS cc_start: 0.6466 (p) cc_final: 0.6156 (p) REVERT: A 686 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8003 (mttp) REVERT: A 740 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7543 (p) REVERT: B 156 ASP cc_start: 0.5311 (t0) cc_final: 0.5105 (OUTLIER) REVERT: B 159 MET cc_start: 0.6975 (mmm) cc_final: 0.6460 (mmm) REVERT: B 283 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: B 447 PHE cc_start: 0.8659 (m-80) cc_final: 0.8442 (m-10) REVERT: B 488 MET cc_start: 0.6551 (mmt) cc_final: 0.6279 (mtm) REVERT: B 562 MET cc_start: 0.9181 (mmt) cc_final: 0.8819 (mmt) REVERT: B 618 ASP cc_start: 0.7175 (m-30) cc_final: 0.6875 (m-30) REVERT: B 619 CYS cc_start: 0.6442 (p) cc_final: 0.6136 (p) REVERT: B 686 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: B 740 THR cc_start: 0.7924 (m) cc_final: 0.7543 (p) REVERT: C 159 MET cc_start: 0.7174 (mmm) cc_final: 0.6324 (mmm) REVERT: C 263 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: C 283 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: C 447 PHE cc_start: 0.8614 (m-80) cc_final: 0.8395 (m-10) REVERT: C 488 MET cc_start: 0.6548 (mmt) cc_final: 0.6270 (mtm) REVERT: C 562 MET cc_start: 0.9181 (mmt) cc_final: 0.8769 (mmt) REVERT: C 618 ASP cc_start: 0.7150 (m-30) cc_final: 0.6856 (m-30) REVERT: C 619 CYS cc_start: 0.6534 (p) cc_final: 0.6224 (p) REVERT: C 686 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: C 740 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7558 (p) REVERT: D 159 MET cc_start: 0.6952 (mmm) cc_final: 0.6426 (mmm) REVERT: D 283 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: D 346 GLN cc_start: 0.9077 (mt0) cc_final: 0.8289 (mt0) REVERT: D 488 MET cc_start: 0.6581 (mmt) cc_final: 0.6313 (mtm) REVERT: D 514 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6622 (mm-40) REVERT: D 562 MET cc_start: 0.9153 (mmt) cc_final: 0.8719 (mmt) REVERT: D 618 ASP cc_start: 0.7129 (m-30) cc_final: 0.6832 (m-30) REVERT: D 619 CYS cc_start: 0.6459 (p) cc_final: 0.6149 (p) REVERT: D 686 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8187 (mttp) REVERT: D 740 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7519 (p) outliers start: 47 outliers final: 26 residues processed: 350 average time/residue: 1.6042 time to fit residues: 625.0547 Evaluate side-chains 333 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 296 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 205 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22222 Z= 0.202 Angle : 0.585 11.925 29822 Z= 0.290 Chirality : 0.038 0.158 3233 Planarity : 0.003 0.032 3600 Dihedral : 15.779 116.641 3885 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.99 % Allowed : 16.16 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2484 helix: 1.62 (0.12), residues: 1620 sheet: 3.09 (0.64), residues: 64 loop : -1.39 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 710 HIS 0.006 0.001 HIS C 301 PHE 0.015 0.001 PHE D 377 TYR 0.014 0.002 TYR A 208 ARG 0.003 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 312 time to evaluate : 2.290 Fit side-chains REVERT: A 283 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: A 447 PHE cc_start: 0.8636 (m-80) cc_final: 0.8428 (m-10) REVERT: A 488 MET cc_start: 0.6570 (mmt) cc_final: 0.6297 (mtm) REVERT: A 562 MET cc_start: 0.9180 (mmt) cc_final: 0.8725 (mmt) REVERT: A 618 ASP cc_start: 0.7213 (m-30) cc_final: 0.6916 (m-30) REVERT: A 619 CYS cc_start: 0.6523 (p) cc_final: 0.6205 (p) REVERT: A 686 LYS cc_start: 0.8843 (ptpp) cc_final: 0.8138 (mttp) REVERT: A 740 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7573 (p) REVERT: B 156 ASP cc_start: 0.5317 (t0) cc_final: 0.5111 (OUTLIER) REVERT: B 159 MET cc_start: 0.7010 (mmm) cc_final: 0.6499 (mmm) REVERT: B 283 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: B 447 PHE cc_start: 0.8647 (m-80) cc_final: 0.8426 (m-10) REVERT: B 488 MET cc_start: 0.6533 (mmt) cc_final: 0.6261 (mtm) REVERT: B 562 MET cc_start: 0.9195 (mmt) cc_final: 0.8817 (mmt) REVERT: B 618 ASP cc_start: 0.7193 (m-30) cc_final: 0.6895 (m-30) REVERT: B 619 CYS cc_start: 0.6499 (p) cc_final: 0.6179 (p) REVERT: B 686 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8192 (mttp) REVERT: B 740 THR cc_start: 0.7903 (m) cc_final: 0.7517 (p) REVERT: C 159 MET cc_start: 0.7080 (mmm) cc_final: 0.6235 (mmm) REVERT: C 263 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: C 283 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: C 447 PHE cc_start: 0.8610 (m-80) cc_final: 0.8393 (m-10) REVERT: C 488 MET cc_start: 0.6559 (mmt) cc_final: 0.6285 (mtm) REVERT: C 562 MET cc_start: 0.9183 (mmt) cc_final: 0.8756 (mmt) REVERT: C 618 ASP cc_start: 0.7169 (m-30) cc_final: 0.6872 (m-30) REVERT: C 619 CYS cc_start: 0.6438 (p) cc_final: 0.6122 (p) REVERT: C 686 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8181 (mttp) REVERT: C 740 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 159 MET cc_start: 0.6962 (mmm) cc_final: 0.6432 (mmm) REVERT: D 283 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 346 GLN cc_start: 0.9088 (mt0) cc_final: 0.8305 (mt0) REVERT: D 488 MET cc_start: 0.6562 (mmt) cc_final: 0.6297 (mtm) REVERT: D 514 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6611 (mm-40) REVERT: D 562 MET cc_start: 0.9159 (mmt) cc_final: 0.8711 (mmt) REVERT: D 618 ASP cc_start: 0.7154 (m-30) cc_final: 0.6857 (m-30) REVERT: D 619 CYS cc_start: 0.6469 (p) cc_final: 0.6156 (p) REVERT: D 686 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8187 (mttp) REVERT: D 740 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7545 (p) outliers start: 44 outliers final: 24 residues processed: 340 average time/residue: 1.5737 time to fit residues: 597.4423 Evaluate side-chains 347 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 312 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 247 optimal weight: 0.4980 chunk 227 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22222 Z= 0.176 Angle : 0.567 11.584 29822 Z= 0.282 Chirality : 0.038 0.157 3233 Planarity : 0.003 0.033 3600 Dihedral : 15.681 118.008 3885 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.71 % Allowed : 16.70 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2484 helix: 1.66 (0.12), residues: 1620 sheet: 3.16 (0.63), residues: 64 loop : -1.40 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 710 HIS 0.006 0.001 HIS C 301 PHE 0.021 0.001 PHE D 377 TYR 0.014 0.002 TYR C 208 ARG 0.003 0.000 ARG C 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 317 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 351 MET cc_start: 0.9224 (mtp) cc_final: 0.9007 (mtp) REVERT: A 447 PHE cc_start: 0.8632 (m-80) cc_final: 0.8425 (m-10) REVERT: A 488 MET cc_start: 0.6562 (mmt) cc_final: 0.6293 (mtm) REVERT: A 562 MET cc_start: 0.9167 (mmt) cc_final: 0.8724 (mmt) REVERT: A 618 ASP cc_start: 0.7203 (m-30) cc_final: 0.6900 (m-30) REVERT: A 619 CYS cc_start: 0.6513 (p) cc_final: 0.6193 (p) REVERT: A 686 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8157 (mttp) REVERT: A 740 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 156 ASP cc_start: 0.5314 (t0) cc_final: 0.5102 (OUTLIER) REVERT: B 159 MET cc_start: 0.6997 (mmm) cc_final: 0.6508 (mmm) REVERT: B 283 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: B 447 PHE cc_start: 0.8642 (m-80) cc_final: 0.8412 (m-10) REVERT: B 488 MET cc_start: 0.6516 (mmt) cc_final: 0.6243 (mtm) REVERT: B 562 MET cc_start: 0.9191 (mmt) cc_final: 0.8837 (mmt) REVERT: B 618 ASP cc_start: 0.7182 (m-30) cc_final: 0.6881 (m-30) REVERT: B 619 CYS cc_start: 0.6475 (p) cc_final: 0.6155 (p) REVERT: B 686 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8165 (mttp) REVERT: B 740 THR cc_start: 0.7888 (m) cc_final: 0.7523 (p) REVERT: C 159 MET cc_start: 0.7073 (mmm) cc_final: 0.6230 (mmm) REVERT: C 263 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: C 283 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: C 447 PHE cc_start: 0.8615 (m-80) cc_final: 0.8396 (m-10) REVERT: C 488 MET cc_start: 0.6543 (mmt) cc_final: 0.6266 (mtm) REVERT: C 562 MET cc_start: 0.9172 (mmt) cc_final: 0.8760 (mmt) REVERT: C 618 ASP cc_start: 0.7172 (m-30) cc_final: 0.6892 (m-30) REVERT: C 686 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8157 (mttp) REVERT: C 740 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7617 (p) REVERT: D 159 MET cc_start: 0.6984 (mmm) cc_final: 0.6458 (mmm) REVERT: D 283 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: D 346 GLN cc_start: 0.9074 (mt0) cc_final: 0.8284 (mt0) REVERT: D 488 MET cc_start: 0.6550 (mmt) cc_final: 0.6283 (mtm) REVERT: D 562 MET cc_start: 0.9147 (mmt) cc_final: 0.8720 (mmt) REVERT: D 618 ASP cc_start: 0.7153 (m-30) cc_final: 0.6862 (m-30) REVERT: D 686 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: D 740 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7516 (p) outliers start: 38 outliers final: 24 residues processed: 343 average time/residue: 1.5660 time to fit residues: 599.7609 Evaluate side-chains 348 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 314 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 205 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126711 restraints weight = 23023.542| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.67 r_work: 0.3295 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22222 Z= 0.200 Angle : 0.585 11.859 29822 Z= 0.290 Chirality : 0.039 0.209 3233 Planarity : 0.003 0.033 3600 Dihedral : 15.706 116.912 3885 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.76 % Allowed : 16.79 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2484 helix: 1.62 (0.12), residues: 1620 sheet: 3.12 (0.63), residues: 64 loop : -1.41 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 710 HIS 0.006 0.001 HIS A 301 PHE 0.013 0.001 PHE B 506 TYR 0.015 0.002 TYR A 208 ARG 0.004 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9750.35 seconds wall clock time: 171 minutes 5.84 seconds (10265.84 seconds total)